scholarly journals Integrating Single-Step GWAS and Bipartite Networks Reconstruction Provides Novel Insights into Yearling Weight and Carcass Traits in Hanwoo Beef Cattle

Animals ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 1836
Author(s):  
Masoumeh Naserkheil ◽  
Abolfazl Bahrami ◽  
Deukhwan Lee ◽  
Hossein Mehrban
Keyword(s):  
Beef Cattle ◽  
Complex Traits ◽  
Genome Wide Association Study ◽  
Additive Genetic Variance ◽  
Carcass Traits ◽  
Single Step ◽  
Bipartite Networks ◽  
Muscle Area ◽  
Eye Muscle ◽  
Network Analyses

In recent years, studies on the biological mechanisms underlying complex traits have been facilitated by innovations in high-throughput genotyping technology. We conducted a weighted single-step genome-wide association study (WssGWAS) to evaluate backfat thickness, carcass weight, eye muscle area, marbling score, and yearling weight in a cohort of 1540 Hanwoo beef cattle using BovineSNP50 BeadChip. The WssGWAS uncovered thirty-three genomic regions that explained more than 1% of the additive genetic variance, mostly located on chromosomes 6 and 14. Among the identified window regions, seven quantitative trait loci (QTL) had pleiotropic effects and twenty-six QTL were trait-specific. Significant pathways implicated in the measured traits through Gene Ontology (GO) term enrichment analysis included the following: lipid biosynthetic process, regulation of lipid metabolic process, transport or localization of lipid, regulation of growth, developmental growth, and multicellular organism growth. Integration of GWAS results of the studied traits with pathway and network analyses facilitated the exploration of the respective candidate genes involved in several biological functions, particularly lipid and growth metabolism. This study provides novel insight into the genetic bases underlying complex traits and could be useful in developing breeding schemes aimed at improving growth and carcass traits in Hanwoo beef cattle.

scholarly journals Multi-Trait Single-Step GBLUP Improves Accuracy of Genomic Prediction for Carcass Traits Using Yearling Weight and Ultrasound Traits in Hanwoo

2021 ◽  
Vol 12 ◽  
Author(s):  
Hossein Mehrban ◽  
Masoumeh Naserkheil ◽  
Deukhwan Lee ◽  
Noelia Ibáñez-Escriche
Keyword(s):  
Beef Cattle ◽  
Carcass Traits ◽  
Single Step ◽  
Birth Date ◽  
Linear Regression Method ◽  
Genomic Information ◽  
Muscle Area ◽  
Eye Muscle ◽  
Correlated Traits ◽  
The Impact

There has been a growing interest in the genetic improvement of carcass traits as an important and primary breeding goal in the beef cattle industry over the last few decades. The use of correlated traits and molecular information can aid in obtaining more accurate estimates of breeding values. This study aimed to assess the improvement in the accuracy of genetic predictions for carcass traits by using ultrasound measurements and yearling weight along with genomic information in Hanwoo beef cattle by comparing four evaluation models using the estimators of the recently developed linear regression method. We compared the performance of single-trait pedigree best linear unbiased prediction [ST-BLUP and single-step genomic (ST-ssGBLUP)], as well as multi-trait (MT-BLUP and MT-ssGBLUP) models for the studied traits at birth and yearling date of steers. The data comprised of 15,796 phenotypic records for yearling weight and ultrasound traits as well as 5,622 records for carcass traits (backfat thickness, carcass weight, eye muscle area, and marbling score), resulting in 43,949 single-nucleotide polymorphisms from 4,284 steers and 2,332 bulls. Our results indicated that averaged across all traits, the accuracy of ssGBLUP models (0.52) was higher than that of pedigree-based BLUP (0.34), regardless of the use of single- or multi-trait models. On average, the accuracy of prediction can be further improved by implementing yearling weight and ultrasound data in the MT-ssGBLUP model (0.56) for the corresponding carcass traits compared to the ST-ssGBLUP model (0.49). Moreover, this study has shown the impact of genomic information and correlated traits on predictions at the yearling date (0.61) using MT-ssGBLUP models, which was advantageous compared to predictions at birth date (0.51) in terms of accuracy. Thus, using genomic information and high genetically correlated traits in the multi-trait model is a promising approach for practical genomic selection in Hanwoo cattle, especially for traits that are difficult to measure.

Identification of genomic regions related to tenderness in Nellore beef cattle

2017 ◽  
Vol 8 (s1) ◽  
pp. s42-s44 ◽  
Author(s):  
M. E. Carvalho ◽  
F. S. Baldi ◽  
M. H. A. Santana ◽  
R. V. Ventura ◽  
G. A. Oliveira ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Genome Wide Association Study ◽  
Additive Genetic Variance ◽  
Single Step ◽  
Meat Tenderness ◽  
Beef Tenderness ◽  
Genome Wide ◽  
Quality Grade ◽  
Nellore Cattle ◽  
Genomic Regions

The aim of this study was to identify genomic regions that associated with beef tenderness in Nellore cattle. Phenotypes were obtained according to the standard USDA Quality Grade (1999). Data from 909 genotyped Nellore bulls were used in the Genome-Wide Association Study (GWAS) undertaken using a single-step approach including also a pedigree file composed of 6276 animals. The analyses were performed using the Blupf90 software, estimating the effect of genomic windows of 10 consecutive markers. The GWAS results identified 18 genomic regions located on 14 different chromosomes (1, 4, 6, 7, 8, 10, 18, 19, 20, 21, 22, 25, 26 and 29), which explained more than 1% of the total additive genetic variance; several candidate genes were located in these regions including SLC2A9, FRAS1, ANXA3, FAM219A, DNAI, AVEN, SHISA7, UBE2S, CDC42EP5, CNTN3, C16orf96, UBALD1, MGRN1 and SNORA1 With the single-step GWAS, it was possible to identify regions and genes related to meat tenderness in Nellore beef cattle.

scholarly journals THI Modulation of Genetic and Non-genetic Variance Components for Carcass Traits in Hanwoo Cattle

2020 ◽  
Vol 11 ◽  
Author(s):  
Yoonji Chung ◽  
Seung Hwan Lee ◽  
Hak-Kyo Lee ◽  
Dajeong Lim ◽  
Julius van der Werf ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Carcass Traits ◽  
Reaction Norm ◽  
Genetic Effects ◽  
Additive Models ◽  
Residual Effects ◽  
Environment Interaction ◽  
Marbling Score ◽  
Muscle Area ◽  
Eye Muscle

The phenotype of carcass traits in beef cattle are affected by random genetic and non-genetic effects, which both can be modulated by an environmental variable such as Temperature-Humidity Index (THI), a key environmental factor in cattle production. In this study, a multivariate reaction norm model (MRNM) was used to assess if the random genetic and non-genetic (i.e., residual) effects of carcass weight (CW), back fat thickness (BFT), eye muscle area (EMA), and marbling score (MS) were modulated by THI, using 9,318 Hanwoo steers (N = 8,964) and cows (N = 354) that were genotyped on the Illumina Bovine SNP50 BeadChip (50K). THI was measured based on the period of 15–45 days before slaughter. Both the correlation and the interaction between THI and random genetic and non-genetic effects were accounted for in the model. In the analyses, it was shown that the genetic effects of EMA and the non-genetic effects of CW and MS were significantly modulated by THI. No significant THI modulation of such effects was found for BFT. These results highlight the relevance of THI changes for the genetic and non-genetic variation of CW, EMA, and MS in Hanwoo beef cattle. Importantly, heritability estimates for CW, EMA, and MS from additive models without considering THI interactions were underestimated. Moreover, the significance of interaction can be biased if not properly accounting for the correlation between THI and genetic and non-genetic effects. Thus, we argue that the estimation of genetic parameters should be based on appropriate models to avoid any potential bias of estimates. Our finding should serve as a basis for future studies aiming at revealing genotype by environment interaction in estimation and genomic prediction of breeding values.

scholarly journals Genomic Prediction Using Alternative Strategies of Weighted Single-Step Genomic BLUP for Yearling Weight and Carcass Traits in Hanwoo Beef Cattle

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 266
Author(s):  
Hossein Mehrban ◽  
Masoumeh Naserkheil ◽  
Deuk Hwan Lee ◽  
Chungil Cho ◽  
Taejeong Choi ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Beef Cattle ◽  
Genomic Prediction ◽  
Quantitative Trait ◽  
Carcass Traits ◽  
Best Linear Unbiased Prediction ◽  
Single Step ◽  
Linear Unbiased Prediction ◽  
Single Nucleotide ◽  
Best Linear Unbiased

The weighted single-step genomic best linear unbiased prediction (GBLUP) method has been proposed to exploit information from genotyped and non-genotyped relatives, allowing the use of weights for single-nucleotide polymorphism in the construction of the genomic relationship matrix. The purpose of this study was to investigate the accuracy of genetic prediction using the following single-trait best linear unbiased prediction methods in Hanwoo beef cattle: pedigree-based (PBLUP), un-weighted (ssGBLUP), and weighted (WssGBLUP) single-step genomic methods. We also assessed the impact of alternative single and window weighting methods according to their effects on the traits of interest. The data was comprised of 15,796 phenotypic records for yearling weight (YW) and 5622 records for carcass traits (backfat thickness: BFT, carcass weight: CW, eye muscle area: EMA, and marbling score: MS). Also, the genotypic data included 6616 animals for YW and 5134 for carcass traits on the 43,950 single-nucleotide polymorphisms. The ssGBLUP showed significant improvement in genomic prediction accuracy for carcass traits (71%) and yearling weight (99%) compared to the pedigree-based method. The window weighting procedures performed better than single SNP weighting for CW (11%), EMA (11%), MS (3%), and YW (6%), whereas no gain in accuracy was observed for BFT. Besides, the improvement in accuracy between window WssGBLUP and the un-weighted method was low for BFT and MS, while for CW, EMA, and YW resulted in a gain of 22%, 15%, and 20%, respectively, which indicates the presence of relevant quantitative trait loci for these traits. These findings indicate that WssGBLUP is an appropriate method for traits with a large quantitative trait loci effect.

The area of eye muscle of beef cattle carcasses

1963 ◽  
Vol 3 (10) ◽  
pp. 249
Author(s):  
RM Seebeck
Keyword(s):  
Beef Cattle ◽  
Cross Sectional Area ◽  
Carcass Weight ◽  
Sectional Area ◽  
Muscle Area ◽  
Cross Sectional ◽  
Eye Muscle ◽  
Angus Cattle ◽  
The Cross

Variations in the cross-sectional area of eye muscle of carcasses cut between the tenth and eleventh ribs were investigated, using 105 Hereford and 51 Angus steers aged 20 months. These cattle consisted of three groups, born in successive years. At constant carcass weight, statistically significant differences in eye muscle area were found between breeds and between years. Breed and year differences were also found in eye muscle area with width and depth of eye muscle constant, so that there are limitations to the estimation of eye muscle area from width and depth measurements. A nomograph is given for estimating eye muscle area from width and depth for Hereford and Angus cattle, when all animals are reared in the same year and environment. The use of eye muscle area as an indicator of weight of carcass muscle is discussed.

scholarly journals Estimation of environmental effects and genetic parameters of carcass traits on Chikso (Korean brindle cattle)

2020 ◽  
Vol 33 (4) ◽  
pp. 525-530 ◽  
Author(s):  
Byoungho Park ◽  
Tae Jeong Choi ◽  
Mi Na Park ◽  
Sang-Hyon Oh
Keyword(s):  
Linear Model ◽  
Environmental Effects ◽  
Genetic Parameters ◽  
Coat Color ◽  
Carcass Traits ◽  
National Level ◽  
Pedigree Information ◽  
Small Scale ◽  
Muscle Area ◽  
Eye Muscle

Objective: The purpose of this study was i) to identify the characteristics of carcass traits in Chikso by gender, region, age at slaughter, and coat color using the carcass data collected from the nationwide pedigree information and coat color investigation, and ii) to estimate genetic parameters for breed improvement.Methods: A linear model was used to analyze the environmental effects on the carcass traits and to estimate genetic parameters. Analysis of variance was performed using TYPE III sum of squares for the unbalanced data provided by the general linear model procedure. Variance components for genetic parameters was estimated using REMLF90 of the BLUPF90 family programs.Results: Phenotypic performance of carcass weight (CW), eye muscle area (EMA), and backfat thickness (BF) in Chikso were lower than those of Hanwoo. This is a natural outcome because Hanwoo have undergone significant efforts for improvement at the national level, a phenomenon not observed in Chikso. Another factor influencing the above outcome was the smaller population size of Chikso compared to that of Hanwoo’s. The heritabilities of CW, EMA, BF, and marbling score in Chikso were estimated as 0.50, 0.37, 0.35, and 0.53, respectively, which were was higher than those of Hanwoo.Conclusion: Based on the genetic parameters that were estimated in this study, it is expected that the carcass traits will improve when the livestock research institutes at each province conduct small-scale performance tests and the semen is provided to farmers after selecting proven bulls using the state-of-art selection technique such as genomic selection.

scholarly journals Effect of boars own performance on progeny fattening and carcass traits in two different environments

2004 ◽  
Vol 20 (3-4) ◽  
pp. 55-63 ◽  
Author(s):  
I. Bahelka ◽  
P. Fľak ◽  
Anna Lukácová
Keyword(s):  
Performance Test ◽  
Average Daily Gain ◽  
Carcass Traits ◽  
Live Weight ◽  
Feed Consumption ◽  
Muscle Area ◽  
Eye Muscle ◽  
Carcass Parameters ◽  
Performance Traits ◽  
Progeny Performance

The effect of own performance traits of meat breed boars on fattening and carcass parameters of progeny in two different test stations (Bucany and Nitra) was evaluated. Own performance traits of boars were average daily gain (ADG) from birth to 100 kg live weight, backfat thickness (BF) and lean meat content (LMC) in field conditions. Progeny of boars was housed in pairs (gilt and barrow) and fed standardized feed mixture semi ad libitum. Progeny test lasted from 30 to 100 kg live weight. There were evaluated following parameters: ADG and feed consumption/kg gain (FC) at test from 30 to 100 kg live weight, slaughter weight (SW), proportion of meaty cuts (PMC) proportion of ham (PHAM), eye muscle area (EMA), and BF. At Bucany and Nitra was found the effect of genotype of boars on progeny BF and/or FC respectively. Better tested boars from own performance test individually as well as a group achieved in progeny better fattening and carcass traits than worse tested boars at Bucany (+33 g ADG, -0.21 cm BF, +2.34 % PMC). Progeny performance from better evaluated boars at Nitra did not exceed the progeny performance from worse tested boars. There was found significant effect of dams on progeny performance.

scholarly journals Genome-wide association study to identify genomic regions and positional candidate genes associated with male fertility in beef cattle

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
H. Sweett ◽  
P. A. S. Fonseca ◽  
A. Suárez-Vega ◽  
A. Livernois ◽  
F. Miglior ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Male Fertility ◽  
Production Efficiency ◽  
Genome Wide Association Study ◽  
Gene Annotation ◽  
Enrichment Analysis ◽  
Single Step ◽  
Positional Candidate ◽  
Functional Candidate Gene

AbstractFertility plays a key role in the success of calf production, but there is evidence that reproductive efficiency in beef cattle has decreased during the past half-century worldwide. Therefore, identifying animals with superior fertility could significantly impact cow-calf production efficiency. The objective of this research was to identify candidate regions affecting bull fertility in beef cattle and positional candidate genes annotated within these regions. A GWAS using a weighted single-step genomic BLUP approach was performed on 265 crossbred beef bulls to identify markers associated with scrotal circumference (SC) and sperm motility (SM). Eight windows containing 32 positional candidate genes and five windows containing 28 positional candidate genes explained more than 1% of the genetic variance for SC and SM, respectively. These windows were selected to perform gene annotation, QTL enrichment, and functional analyses. Functional candidate gene prioritization analysis revealed 14 prioritized candidate genes for SC of which MAP3K1 and VIP were previously found to play roles in male fertility. A different set of 14 prioritized genes were identified for SM and five were previously identified as regulators of male fertility (SOD2, TCP1, PACRG, SPEF2, PRLR). Significant enrichment results were identified for fertility and body conformation QTLs within the candidate windows. Gene ontology enrichment analysis including biological processes, molecular functions, and cellular components revealed significant GO terms associated with male fertility. The identification of these regions contributes to a better understanding of fertility associated traits and facilitates the discovery of positional candidate genes for future investigation of causal mutations and their implications.

scholarly journals Growth Performance and Carcass Traits Responses to Dried Distillers’ Grain with Solubles Feeding of Growing Awassi Ram Lambs

Animals ◽  
2019 ◽  
Vol 9 (11) ◽  
pp. 954 ◽  
Author(s):  
Safa’ M. Hatamleh ◽  
Belal S. Obeidat
Keyword(s):  
Meat Quality ◽  
Control Diet ◽  
Average Daily Gain ◽  
Carcass Traits ◽  
Quality Parameters ◽  
Muscle Area ◽  
Eye Muscle ◽  
Distillers Grain ◽  
Dried Distillers Grain ◽  
The Impact

This study considers the impact of dried distillers’ grain with solubles (DDGS) in diets of lambs. Randomly; 27 lambs were distributed to one of three diets. Diets were: a control diet (CON; n = 9), a 125 (DDGS125; n = 9) or a 250 g/kg DDGS (DDGS250; n = 9) of dietary dry matter (DM). The lambs were fed using these diets for 91 days. To assess carcass traits; five lambs were randomly selected at the end of the study. No significant differences were detected in intake and digestibility of DM; crude protein and fiber. Average daily gain did not differ among diets. Carcass characteristics did not differ among diets. With the exception of shear force and redness, which were greater in DDGS250 than in DDGS125 and CON diets, meat quality parameters were unaffected. Eye muscle area decreased in DDGS125 than in DDGS250 and CON diet. These results demonstrate that the feeding of lambs on DDGS at 125 or 250 g/kg DM did not have any impact on growth. These diets only had a simple effect on the characteristics of carcass and meat quality. These results suggest that it would be suitable to introduce these feeds into sheep nutrition in the future.

Detection of candidate genes for growth and carcass traits using genome-wide association strategy in Chinese Simmental beef cattle

2018 ◽  
Vol 58 (2) ◽  
pp. 224 ◽  
Author(s):  
Wengang Zhang ◽  
Lingyang Xu ◽  
Huijiang Gao ◽  
Yang Wu ◽  
Xue Gao ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Average Daily Gain ◽  
Carcass Traits ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Economic Traits ◽  
Cattle Industry ◽  
Genome Wide

In Chinese beef cattle industry, there are more than 60 million livestock, nearly half of which are Chinese Simmental beef cattle or Simmental crossbreds. Over the past decades, numerous quantitative trait loci for economic traits in cattle have been identified, while few studies for growth and carcass traits have been reported in Simmental beef cattle. In the present study, we conducted genome-wide association study based on BovineHD BeadChip and identified 41, 15, 3, 22 and 16 single-nucleotide polymorphisms significantly associated with average daily gain, liveweight before slaughter, carcass weight, dressing percentage and pure meat percentage respectively. In total, 18 candidate genes were found for growth and carcass traits, and four haplotype blocks for growth and carcass traits were discovered. These findings will facilitate detection of major genes and genetic variants involved in growth and carcass traits of beef cattle in further studies.

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